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<h1>Spectral deconvolution / Multivariate Curve Resolution</h1>

<p>
    This method performs Spectral Deconvolution of detected peaks. It finds components (compounds, analytes, etc.) and
    determines their model peaks and fragmentation mass spectra.
</p>
<p>
    The spectral deconvolution uses both constructed chromatograms and detected peaks. The list of constructed
    chromatograms is specified by selecting <i>Specific peak lists</i> for parameter <em>Chromatograms</em>, clicking
    on the ellipsis button, and choosing one or more lists with chromatograms in the popup window. The list of
    detected peaks is specified by selecting <i>Specific peak lists</i> for parameter <em>Peaks</em>, clicking on the
    ellipsis button, and choosing one or more lists with detected peaks in the popup window.
</p>

<p>
<div align="center">
    <img src="spectral_deconvolution_window.png" alt="Spectral Deconvolution Window">
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</p>

<p>
    The Spectral Deconvolution consists of two steps:
</p>
<ol>
    <li>
        <p>Entire retention time interval is split into deconvolution windows so that
        <p/>
        <ul>
            <li>Peaks produced by the same component or by coeluting components belong to the same deconvolution
                window,
            </li>
            <li>Number of peaks in deconvolution window is significantly smaller than the total number of peaks.</li>
        </ul>
        <p>
            The deconvolution windows are displayed in the top plot of the preview, where small dash lines denote peaks
            in the (retention time, m/z)-plane, and peaks belonging to one deconvolution window have the same color.
            The vertical sequences of peaks usually mark the presence of one or several compounds, so it is important
            that those peaks are assigned to the same deconvolution window, i.e. they have the same color on the plot.
            On
            the other hand, if deconvolution windows contain too many peaks, it will significantly <b>slow down</b> the
            spectral
            deconvolution computations, so the deconvolution windows should be as short (in the retention time domain)
            as
            possible.
        </p>
        <p>The following parameter controls the deconvolution window selection:</p>
        <ul>
            <li><em>Deconvolution window width (min)</em> - The algorithm will
                produce deconvolution windows so that their width (in retention time domain) does not exceed the value
                of this parameter.
            </li>
        </ul>
    </li>

    <li>
        <p>
            The algorithm infers the number of components in each deconvolution window and construct their
            model peaks and fragmentation spectra. The inferred number of components is controlled by three parameters:
        </p>
        <ul>
            <li><em>Retention time tolerance (min)</em> - The smallest time-gap between any two components,</li>
            <li><em>Minimum Number of Peaks</em> - The smallest number of detected peaks to form a component,</li>
            <li><em>Adjust Apex Ret Times</em> - If this parameter is false, then the retention time of each detected
                peak is determined by the retention time of its highest data point. If this parameter is true, then
                the retention time of each detected peak is determined by fitting a parabola into the top half of that
                peak.
            </li>
        </ul>
    </li>
</ol>


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